tilt series import and alignment

[Jason K]

Hello all,

Does e2tomogram.py have any internals that assume light-on-dark or dark-on-light such that the --invert flag in e2import.py would have an effect on downstream processing?

Under what circumstances would I want to change pk_mindist and/or npk?

I would like to compute a suitable value for --bxsz from manual inspection of the unaligned tilt series. How should I do this?

Best,

Jason

[Steve Ludtke]

Yes!  Tilt series must be dark on white. Everything else is the opposite convention.

Normally the default values are fine for everything else. If you are having problems with poor alignments (and have dark on white tilt series), then you might need to tweak something, but in my experience this is extremely rare.  If you do find counterexamples and are willing to share, they are extremely valuable in testing and improving the defaults.

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[Muyuan Chen]

1. Dark density in light background. It will invert when generating particles.

2. Smaller npk for tilt series with only a few gold beads is sometimes better. While it can use other features , the precision might be lower. I don’t even recall the pk_mindist option and haven’t changed that ever..

3. Not sure what this means... maybe just play with different numbers first? 

On Jan 23, 2021, at 8:54 PM, Jason K <jt...@cornell.edu> wrote:

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[Jason K]

That may explain why my series were not aligning well...haha

The convention difference was sufficiently surprising to me as a long-time EMAN2 user that I suggest adding a sentence to https://blake.bcm.edu/emanwiki/EMAN2/e2tomo subheading "For your own data:"

Thanks for the quick response!